transcription & RNA processing

This study shows HSF1 enhances c-MYC transcription independently of the heat-shock response by recruiting GCN5 to promote histone acetylation.

This study shows MYC regulates RNA polymerase II methylation and transcription termination through interaction with PRMT5, and its inhibition affects gene expression in cancer cells.

This study identifies lipid-dependent and lipid-independent mechanisms by which BASP1 modifies chromatin and represses transcription, with implications for its tumor suppressor function.

This study shows that BORIS/CTCFL alters chromatin accessibility in melanoma cells, promoting a pro-invasive transcriptional signature by upregulating invasion genes and downregulating tumor suppressors.

This study shows that Rho, a transcription termination factor, regulates stationary phase adaptation in B. subtilis by affecting Spo0A, AbrB, and CodY regulons, and blocks sporulation and competence.

This study identifies NDP52's role in modulating RNA Polymerase II transcription by altering DNA conformation through direct dsDNA binding and interactions with chromatin regulators.

The paper identifies HOXD13 as a direct target of EWS-FLI1 and shows it modulates transcriptional states in Ewing sarcoma by antagonizing EWS-FLI1-dependent gene repression.

This study shows that a single cycle of transient OSKM expression reverses aging-related DNA methylation, transcriptional, and metabolic changes in multiple tissues of aged mice.

This paper describes an upgraded consumer 3D printer for bioprinting tumor models with tunable mechanical properties and validated cell viability.

The paper uses single-cell RNA-sequencing to analyze iNKT cell activation states over time, identifying a cMAF-associated transcriptional state in NKT10 cells.

This paper develops a spatial stochastic model to show how supercoiling affects transcription regulation in E. coli by enabling communication between RNA polymerase molecules and coordinating gene expression.

This study develops 3D bioprinted scaffolds using agarose-hydroxyapatite and graphene oxide to enhance bone regeneration, showing improved osteogenic marker expression and ECM mineralization.

This study uses direct RNA sequencing to analyze RSV mRNA transcripts in infected cells, revealing gene abundance patterns and polyadenylate tail lengths.

This study examines how drought stress affects hybrid poplar transcriptomes and physiology, finding that time of day and drought severity significantly influence responses.

This study investigates how transcriptional and post-transcriptional mechanisms regulate young genes in plants, finding that they are expressed at low levels and subject to additional decay processes.

The paper compares somatic TADs in chicken fibroblasts with lampbrush chromomere-loop complexes in chicken oocytes, finding that genomic regions from different TADs can localize to the same chromomere-loop complex.

This paper develops a cell fiber-based culture system for primary rat hepatocytes, demonstrating their proliferation and functional maintenance over 30 days, with applications in drug sensing and transplantation.

SCATrEx maps single-cell transcriptomes to copy number evolutionary trees, revealing clone-specific gene expression heterogeneity in tumors.

This study shows that Arp2/3 complex activity is necessary for morphology changes during mESC differentiation, regulates differentiation markers, and enables lineage specification.

The paper studies transcriptional bursting at the p21 gene and identifies short-term transcriptional memory (STTM) linked to p53 regulation and burst duration.

The paper identifies a transcriptional repressor cascade downstream of Wnt signaling that controls hepatocyte cell cycle progression by repressing E2F7 and E2F8.

The paper identifies proteasome-associated HECT-type ubiquitin ligases that relay and process hormone-specific transcriptional activators, regulating their activity and stability.

The paper identifies light-responsive genes regulated by PIF and shows that chromatin changes, specifically H3K9 acetylation, parallel rapid transcriptional responses to light.

Enformer, a sequence-based transformer integrating elements up to 100 kb away, lifts held-out gene expression prediction (correlation 0.81 to 0.85 versus Basenji2) and variant effect prediction.

This study identifies how EWS/FLI fusion proteins alter chromatin structure and transcription in Ewing sarcoma, highlighting their role in reprogramming 3D chromatin to drive transcriptional changes.

This study identifies antigen-specific transcriptional programs in follicular helper T cells across effector function and memory development, revealing distinct inflammatory and anti-inflammatory modules.

The paper quantifies global trait variation in trees, identifying two independent processes and seven key traits that capture most variation in tree form and function.

The paper develops BaRTv2.18, a highly resolved barley reference transcriptome, improving transcript diversity and quantification accuracy over previous versions.

This study shows that miRNA biogenesis in plants is coupled to transcription through R-loops, which anchor transcripts and promote co-transcriptional processing.